You shouldn't have to configure using sudo if the netcdf file is in your home directory, which it looks like it is, since it is on your desktop. You should have write access to that as an ordinary user. That said, no running it with sudo shouldn't hurt -- presumably that command worked without error and hence you have root access?

The next command is usually make, sudo make install being third (just putting it into the binaries). That is, the command sequence is usually.

./configuremakesudo make install

All from the directory you specify. This compiles the package from source, which can be tricky to get to work. You mentioned you are on ubuntu. Have you tried simply issuing:

sudo apt-get install netcdf-bin

at the command-line instead? That should install the software, automatically resolve dependencies you might be missing, and be easier to keep it up to date.

Jason-
The problem almost certainly is that you do not have
access to /usr/local.
You will need to do one of two things.
1. configure and install netcdf using sudo or logged in as root.
2. choose a different location to install netcdf; one for which you
have write access. You specify that by saying
./configure -prefix=<path to install directory>